Can you keep the folder on your lap, if the luggage rack is full?
Every car in Amtrak (NEC) has a section where people put the suitcases. I've yet to see this section so full where you could not put your folder there. If this is the case, you simply move to the next car and the next. The luggage rack above your head is usually not accepted. IF YOU Absolutely must, I suspose it could sit on your lap. However, this will become very concomfortable and your're better off standing by the door with your folder.
It shouldn't be a problem so don't worry.